TFBS in overlapping upstream regions in Bacteria

Question

[Juan Cordero]

Dear community,

In order to find novel TFBS I am searching for some motifs in upstream regions.

Some upstream sequences in the forward strand overlap with coding sequences in the reverse strand. Should I also consider such sequences? Would you expect differences in GC% in overlapping from non-overlapping TFBS?

Thanks

Answer 1

[dago]

I found the following paper really interesting in this regards.

http://www.sciencedirect.com/science/article/pii/S0378111912003770#

Maybe it helps you.